Allow patterns in file paths (#51)

* Add resolution function to common

* Use resolution function in assertion and case

* Add unit tests

* Update CHANGELOG

* Update version

* Address linter

* Clearer error message and remove assert

* Update tests to include unit test for resolve_single_path function

* Remove parenthesis

* Remove unnecessary str

* Update test to instantiate NFTestAssert

CHANGELOG.md

@@ -11,6 +11,12 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ---
 
+## [1.0.0] - 2023-10-23
+### Added
+- Support for patterns in expected and actual file paths
+
+---
+
 ## [1.0.0-rc.4] - 2023-10-04
 ### Changed
 - Wrap all NextFlow output with real-time line-by-line log statements

nftest/NFTestAssert.py

@@ -4,12 +4,11 @@
 import os
 import selectors
 import subprocess as sp
-from pathlib import Path
 from subprocess import PIPE
 from typing import Callable
 from logging import getLogger, DEBUG, ERROR
 
-from nftest.common import calculate_checksum
+from nftest.common import calculate_checksum, resolve_single_path
 from nftest.NFTestENV import NFTestENV
 
 
@@ -19,13 +18,18 @@ def __init__(self, actual:str, expect:str, method:str='md5', script:str=None):
         """ Constructor """
         self._env = NFTestENV()
         self._logger = getLogger('NFTest')
-        self.actual = Path(actual)
-        self.expect = Path(expect)
+        self.actual = actual
+        self.expect = expect
         self.method = method
         self.script = script
 
         self.startup_time = datetime.datetime.now(tz=datetime.timezone.utc)
 
+    def identify_assertion_files(self) -> None:
+        """ Resolve actual and expected paths """
+        self.actual = resolve_single_path(self.actual)
+        self.expect = resolve_single_path(self.expect)
+
     def assert_exists(self) -> None:
         "Assert that the expected and actual files exist."
         if not self.actual.exists():

nftest/NFTestCase.py

@@ -84,6 +84,7 @@ def test(self):
             return
         for ass in self.asserts:
             try:
+                ass.identify_assertion_files()
                 ass.assert_exists()
                 ass.assert_updated()
                 ass.assert_expected()

nftest/__init__.py

@@ -1,3 +1,3 @@
 """ nftest module """
 
-__version__ = '1.0.0-rc.4'
+__version__ = '1.0.0'

nftest/common.py

@@ -27,6 +27,15 @@ def remove_nextflow_logs() -> None:
         else:
             os.remove(file)
 
+def resolve_single_path(path:str) -> Path:
+    """ Resolve wildcards in path and ensure only a single path is identified """
+    expanded_paths = glob.glob(path)
+    if 1 != len(expanded_paths):
+        raise ValueError(f"Path `{path}` resolved to 0 or more than 1 file: {expanded_paths}." \
+        " Assertion failed.")
+
+    return Path(expanded_paths[0])
+
 def calculate_checksum(path:Path) -> str:
     """ Calculate checksum recursively.
     Args:

test/unit/test_NFTestAssert.py

@@ -101,3 +101,34 @@ def test_assert_expected(mock_assert):
     mock_assert.return_value.get_assert_method = lambda: lambda x, y: False
     with pytest.raises(AssertionError):
         NFTestAssert.assert_expected(mock_assert())
+
+@pytest.mark.parametrize(
+    'glob_return_value,case_pass',
+    [
+        ([], False),
+        (['a', 'b'], False),
+        (['a'], True)
+    ]
+)
+@mock.patch('glob.glob')
+@mock.patch('nftest.NFTestAssert.NFTestENV')
+@mock.patch('logging.getLogger')
+def test_identify_assertions_files(
+    mock_getlogger,
+    mock_env,
+    mock_glob,
+    glob_return_value,
+    case_pass):
+    ''' Tests for proper file identification '''
+
+    mock_glob.return_value = glob_return_value
+    mock_env.return_value = None
+    mock_getlogger.return_value = lambda x: None
+
+    test_assert = NFTestAssert('', '')
+
+    if case_pass:
+        test_assert.identify_assertion_files()
+    else:
+        with pytest.raises(ValueError):
+            test_assert.identify_assertion_files()

test/unit/test_common.py

@@ -0,0 +1,27 @@
+# pylint: disable=W0212
+''' Test module for common functions '''
+
+import mock
+import pytest
+
+from nftest.common import resolve_single_path
+
+@pytest.mark.parametrize(
+    'glob_return_value,case_pass',
+    [
+        ([], False),
+        (['a', 'b'], False),
+        (['a'], True)
+    ]
+)
+@mock.patch('glob.glob')
+def test_resolve_single_path(mock_glob, glob_return_value, case_pass):
+    ''' Tests for proper file identification '''
+    test_path = '/some/path'
+    mock_glob.return_value = glob_return_value
+
+    if case_pass:
+        resolve_single_path(test_path)
+    else:
+        with pytest.raises(ValueError):
+            resolve_single_path(test_path)